Params: ./cmzasha --no-stderr --filter 100 30 Rfam/cm/RF00053.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00053_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin Build: release Host: recycle.cs.washington.edu pid: 8873 ----cmFile: Rfam/cm/RF00053.cm (global) ----fastaFile: /projects/bio/zasha/seqs/embl/fun.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/inv01.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/inv01.dat.fasta.gz ----sequence: #5507,sp|AC007837.4|AC007837 Drosophila melanogaster, chromosome 2R, region 57B2-B3, BAC clone BACR04I07, complete sequence. ----isReversed: 0 ----hitSequence: GAGUGCAUUCCGUAUGGAAGACUAGUGAUUUUGUUGUUUGGUCUUUGGUAAUAACAAUAAAUCCCUUGUCUUCUUACGGCGUGCAUUU hit 0 : 16002 16089 (fwd) 34.57 bits :<<<<<<<<<<<<<-<<-------<<<<<-<<<<<<<<____________._>>>>>>>> 1 gaguuaguuccaugUggAAGACUAgugauUuuguuguuuUguuaUugcUA.ugacaacaa 59 GA:U:::UUCC:U:UG:AAGACUAG:GAUUUU:UUGU:U GU+ UUG+UA U:ACAA:AA 16002 GAGUGCAUUCCGUAUGGAAGACUAGUGAUUUUGUUGUUUGGUCUUUGGUAaUAACAAUAA 16061 >>>>>------>>->>>>>>>>>>>>>: 60 aucacAGuCugccUcauggcgcagacuc 87 AUC:C :CU:A:GGCG:::A:U 16062 AUCCCUUGUCUUCUUACGGCGUGCAUUU 16089 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/inv01.dat.fasta.gz ----sequence: #5702,sp|AC009218.7|AC009218 Drosophila melanogaster, chromosome 2R, region 57B-57B, BAC clone BACR33D17, complete sequence. ----isReversed: 0 ----hitSequence: GAGUGCAUUCCGUAUGGAAGACUAGUGAUUUUGUUGUUUGGUCUUUGGUAAUAACAAUAAAUCCCUUGUCUUCUUACGGCGUGCAUUU hit 1 : 49108 49195 (fwd) 34.57 bits :<<<<<<<<<<<<<-<<-------<<<<<-<<<<<<<<____________._>>>>>>>> 1 gaguuaguuccaugUggAAGACUAgugauUuuguuguuuUguuaUugcUA.ugacaacaa 59 GA:U:::UUCC:U:UG:AAGACUAG:GAUUUU:UUGU:U GU+ UUG+UA U:ACAA:AA 49108 GAGUGCAUUCCGUAUGGAAGACUAGUGAUUUUGUUGUUUGGUCUUUGGUAaUAACAAUAA 49167 >>>>>------>>->>>>>>>>>>>>>: 60 aucacAGuCugccUcauggcgcagacuc 87 AUC:C :CU:A:GGCG:::A:U 49168 AUCCCUUGUCUUCUUACGGCGUGCAUUU 49195 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/inv01.dat.fasta.gz ----sequence: #7807,sp|AE003791.4|AE003791 Drosophila melanogaster chromosome 2R, section 59 of 74 of the complete sequence. ----isReversed: 0 ----hitSequence: GAGUGCAUUCCGUAUGGAAGACUAGUGAUUUUGUUGUUUGGUCUUUGGUAAUAACAAUAAAUCCCUUGUCUUCUUACGGCGUGCAUUU hit 2 : 91950 92037 (fwd) 34.57 bits :<<<<<<<<<<<<<-<<-------<<<<<-<<<<<<<<____________._>>>>>>>> 1 gaguuaguuccaugUggAAGACUAgugauUuuguuguuuUguuaUugcUA.ugacaacaa 59 GA:U:::UUCC:U:UG:AAGACUAG:GAUUUU:UUGU:U GU+ UUG+UA U:ACAA:AA 91950 GAGUGCAUUCCGUAUGGAAGACUAGUGAUUUUGUUGUUUGGUCUUUGGUAaUAACAAUAA 92009 >>>>>------>>->>>>>>>>>>>>>: 60 aucacAGuCugccUcauggcgcagacuc 87 AUC:C :CU:A:GGCG:::A:U 92010 AUCCCUUGUCUUCUUACGGCGUGCAUUU 92037 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/inv02.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/inv03.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/mam.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/mus.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/mus.dat.fasta.gz ----sequence: #4664,sp|AC026385.19|AC026385 Mus musculus 17 BAC RP23-413K14 complete sequence. ----isReversed: 0 ----hitSequence: GAGCCAGUGCUAUGUGGAAGACUUGUGAUUUUGUUGUUCUGAUAUGAUAUGACAACAAGUCACAGCCAGCCUCAUAGCGUGGACUC hit 3 : 122238 122323 (fwd) 35.90 bits :<<<<<<<<<<<<<-<<-------<<<<<-<<<<<<<<_____________>>>>>>>>> 1 gaguuaguuccaugUggAAGACUAgugauUuuguuguuuUguuaUugcUAugacaacaaa 60 GAG::+:U:C:AUGUGGAAGACU GUGA:UUUGUUGUU+UG+UAU G UAUGACAACAA: 122238 GAGCCAGUGCUAUGUGGAAGACUUGUGAUUUUGUUGUUCUGAUAU-GAUAUGACAACAAG 122296 >>>>------>>->>>>>>>>>>>>>: 61 ucacAGuCugccUcauggcgcagacuc 87 UCACAG+C GCCUCAU:G:G:+::CUC 122297 UCACAGCCAGCCUCAUAGCGUGGACUC 122323 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/org.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/phg.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/pln.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/pro02.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/pro03.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/pro04.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/pro05.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/rod.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/vrt.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/vrt.dat.fasta.gz ----sequence: #24261,sp|AL929155.4|AL929155 Zebrafish DNA sequence from clone DKEY-265M8 ----isReversed: 0 ----hitSequence: UAUUUUGGGCAUUAUGGAAGACUAGUGAUUUUGUUGUUGUGACGUCAUCAGUACUGACAACAAGUCACAGUCUGCCUCAGUGACCAGAAUC hit 4 : 163041 163131 (fwd) 37.29 bits :<<<<<<<<<<<<<-<<-------<<<<<-<<<<<<<<__...__________._>>>>> 1 gaguuaguuccaugUggAAGACUAgugauUuuguuguuuU...guuaUugcUA.ugacaa 56 A:UU:G::C::U:UGGAAGACUAGUGA:UUUGUUGUU+U GU+AU ++UA UGACAA 163041 UAUUUUGGGCAUUAUGGAAGACUAGUGAUUUUGUUGUUGUgacGUCAUCAGUAcUGACAA 163100 >>>>>>>>------>>->>>>>>>>>>>>>: 57 caaaucacAGuCugccUcauggcgcagacuc 87 CAA:UCACAGUCUGCCU:A::G::C:GA:UC 163101 CAAGUCACAGUCUGCCUCAGUGACCAGAAUC 163131 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/hum01.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/hum02.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/hum02.dat.fasta.gz ----sequence: #734,sp|AC005523.1|AC005523 Homo sapiens chromosome 19, cosmid R28154, complete sequence. ----isReversed: 0 ----hitSequence: GGUCUAGUGCUGUGUGGAAGACUAGUGAUUUUGUUGUUCUGAUGUACUACGACAACAAGUCACAGCCGGCCUCAUAGCGCAGACUC hit 5 : 3567 3652 (fwd) 37.65 bits :<<<<<<<<<<<<<-<<-------<<<<<-<<<<<<<<_____________>>>>>>>>> 1 gaguuaguuccaugUggAAGACUAgugauUuuguuguuuUguuaUugcUAugacaacaaa 60 G:::UAGU:C::UGUGGAAGACUAGUGA:UUUGUUGUU+UG+U U +CUA+GACAACAA: 3567 GGUCUAGUGCUGUGUGGAAGACUAGUGAUUUUGUUGUUCUGAUGU-ACUACGACAACAAG 3625 >>>>------>>->>>>>>>>>>>>>: 61 ucacAGuCugccUcauggcgcagacuc 87 UCACAG+C GCCUCA::G:GCAG:::C 3626 UCACAGCCGGCCUCAUAGCGCAGACUC 3652 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/hum02.dat.fasta.gz ----sequence: #1382,sp|AC006537.1|AC006537 Homo sapiens chromosome 19, cosmid R30140, complete sequence. ----isReversed: 0 ----hitSequence: GGUCUAGUGCUGUGUGGAAGACUAGUGAUUUUGUUGUUCUGAUGUACUACGACAACAAGUCACAGCCGGCCUCAUAGCGCAGACUC hit 6 : 35676 35761 (fwd) 37.65 bits :<<<<<<<<<<<<<-<<-------<<<<<-<<<<<<<<_____________>>>>>>>>> 1 gaguuaguuccaugUggAAGACUAgugauUuuguuguuuUguuaUugcUAugacaacaaa 60 G:::UAGU:C::UGUGGAAGACUAGUGA:UUUGUUGUU+UG+U U +CUA+GACAACAA: 35676 GGUCUAGUGCUGUGUGGAAGACUAGUGAUUUUGUUGUUCUGAUGU-ACUACGACAACAAG 35734 >>>>------>>->>>>>>>>>>>>>: 61 ucacAGuCugccUcauggcgcagacuc 87 UCACAG+C GCCUCA::G:GCAG:::C 35735 UCACAGCCGGCCUCAUAGCGCAGACUC 35761 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/hum02.dat.fasta.gz ----sequence: #4356,sp|AC013489.17|AC013489 Homo sapiens chromosome 15, clone RP11-97O12, complete sequence. ----isReversed: 1 ----hitSequence: CGGCUGGCCCCAUCUGGAAGACUAGUGAUUUUGUUGUUGUCUUACUGCGCUCAACAACAAAUCCCAGUCUACCUAAUGGUGCCAGCCA hit 7 : 21820 21733 (rev) 37.45 bits :<<<<<<<<<<<<<-<<-------<<<<<-<<<<<<<<____________._>>>>>>>> 1 gaguuaguuccaugUggAAGACUAgugauUuuguuguuuUguuaUugcUA.ugacaacaa 59 :G:::G::CCAU:UGGAAGACUAG:GAUUUUGUUGU:+U UUA UGC +:ACAACAA 154017 CGGCUGGCCCCAUCUGGAAGACUAGUGAUUUUGUUGUUGUCUUACUGCGCuCAACAACAA 154076 >>>>>------>>->>>>>>>>>>>>>: 60 aucacAGuCugccUcauggcgcagacuc 87 AUC:CAGUCU CCU:AUGG::C:::C:+ 154077 AUCCCAGUCUACCUAAUGGUGCCAGCCA 154104 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/hum03.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/hum03.dat.fasta.gz ----sequence: #2806,sp|AC104259.14|AC104259 Homo sapiens chromosome 15, clone CTD-2525I4, complete sequence. ----isReversed: 1 ----hitSequence: CGGCUGGCCCCAUCUGGAAGACUAGUGAUUUUGUUGUUGUCUUACUGCGCUCAACAACAAAUCCCAGUCUACCUAAUGGUGCCAGCCA hit 8 : 97327 97240 (rev) 37.45 bits :<<<<<<<<<<<<<-<<-------<<<<<-<<<<<<<<____________._>>>>>>>> 1 gaguuaguuccaugUggAAGACUAgugauUuuguuguuuUguuaUugcUA.ugacaacaa 59 :G:::G::CCAU:UGGAAGACUAG:GAUUUUGUUGU:+U UUA UGC +:ACAACAA 58427 CGGCUGGCCCCAUCUGGAAGACUAGUGAUUUUGUUGUUGUCUUACUGCGCuCAACAACAA 58486 >>>>>------>>->>>>>>>>>>>>>: 60 aucacAGuCugccUcauggcgcagacuc 87 AUC:CAGUCU CCU:AUGG::C:::C:+ 58487 AUCCCAGUCUACCUAAUGGUGCCAGCCA 58514 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/hum04.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/hum05.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/hum06.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/hum07.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/hum08.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/hum09.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/hum10.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/hum10.dat.fasta.gz ----sequence: #1519,sp|AL354733.15|AL354733 Human DNA sequence from clone RP11-575L7 on chromosome 9 ----isReversed: 1 ----hitSequence: GGCCUAGUUCUGUGUGGAAGACUAGUGAUUUUGUUGUUUUUAGAUAACUAAAUCGACAACAAAUCACAGUCUGCCAUAUGGCACAGGCCA hit 9 : 170740 170651 (rev) 36.31 bits :<<<<<<<<<<<<<-<<-------<<<<<-<<<<<<<<____________..._>>>>>> 1 gaguuaguuccaugUggAAGACUAgugauUuuguuguuuUguuaUugcUA...ugacaac 57 G:::UAG:UC::U:UGGAAGACUAGUGAUUUUGUUGUUUU + AU++CUA +GACAAC 18840 GGCCUAGUUCUGUGUGGAAGACUAGUGAUUUUGUUGUUUUUAGAUAACUAaauCGACAAC 18899 >>>>>>>------>>->>>>>>>>>>>>>: 58 aaaucacAGuCugccUcauggcgcagacuc 87 AAAUCACAGUCUGCC :A::GC:CAG:::+ 18900 AAAUCACAGUCUGCCAUAUGGCACAGGCCA 18929 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/hum11.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/hum12.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/hum13.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/hum14.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/hum15.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/hum16.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/hum17.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/hum18.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/hum19.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/hum20.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/hum21.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/hum22.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/hum23.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/hum24.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/hum25.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/hum26.dat.fasta.gz done 1.65905e+10 nucs (frac lets thru so far=6.50974e-08, 2d-fracLetsThru=3.55757e-08). Filter report: done 1.65905e+10 nucs (frac lets thru so far=6.50974e-08, 2d-fracLetsThru=3.55757e-08). done 1.65905e+10 nucs (frac lets thru so far=6.50974e-08, 2d-fracLetsThru=3.55757e-08). CPU time: 292637.28u 1055.86s 81:34:53.14 Elapsed: 85:06:10